Reptile & Amphibian Forums

In my original post about the virtues of inbreeding, my friend Jeff demonstrated a common fallacious belief among educated animal breeders. This fallacy is the notion that inbreeding causes an increase in the prevalence of defective and deleterious genes in populations in which it occurs.

Yes, inbreeding, particularly repetitive inbreeding, can result in gene loss in populations. But, we already concluded that gene loss can't cause the appearance of defective genes in populations. Gene loss depletes populations of genes and their associated traits, traits that may be helpful in enabling the population to adapt to environmental changes.

Conditions such as dwarfism, albinism, and anophthalmia (absence of eyes) result from mutations in individuals within populations. These mutations can be point mutations or deletion mutations (or other types of mutations as well). Inbreeding by itself has no effect on the generation of mutations within populations.

Inbreeding CAN cause the APPEARANCE of recessive genetic DISORDERS resulting from mutant or defective genes in populations in which these mutant genes ALREADY EXIST. Most people remember learning in grade school about the appearance of hemophelia in inbred human populations. Rare defective genes for recessive genetic disorders such as hemophelia only rarely show themselves in populations where no inbreeding occurs. This is because any individuals that by rare occurance inherit one copy of the defective gene still have one good copy of the gene (and are thus normal). Remember, we all have two copies of most of our genes (one from our mother and the other from our father). If one is defective, the other one usually can still do the job.

When inbreeding occurs, there is a greater likelihood of individual progeny within inbred populations harboring defective copies in both the maternally and paternally inherited gene. Thus rare genetic disorders can appear in inbred populations. The abundance of mutant or defective genes is not greater in these populations. Inbreeding won't cause new mutant genes to arise. What is different in inbred populations is that the appearance of individuals with rare, recessive genetic conditions can be increased.

Robert Bruce.

Spoken like a molecular biologist!

Another thing to consider - some genes that may be delterious to the general population when expressed, stick around because they confer a benefit under certain circumstances. If I remember correctly, Sickle Cell Anemia causes problems for people of African origin. However, the gene also confers a degree of resistance to Malaria, even when not expressed. Thus the gene confers a survival advantage on the overall population, even though some individuals (who get both genes) are at a disadvantage.

So genes that cause dwarfism, albanism, etc. may persist in the Indigo population (and other snakes for that matter), confering some benefit(s) we don't yet understand.

Regards,

John D.
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I am so not lesdysxic!

0.1 Creamsicle Cornsake "Yolanda"
1.0 Bairds Ratsnake "Steely Dan"
0.1 Desert Kingsnake "FATTY"

Actually I must disagree about inbreeding. As I have stated earlier, we see a general "weakening" in rodents and Ceriodaphnia in continued inbreeding populations. Even with continued cell passaging there is a general "loss of viability" of the cells.

Inbreeding depression encompasses a wide variety of physical and health defects. Any given inbred animal generally has several, but not all, of these defects. These defects include:

>Elevated incidence of recessive genetic diseases

>Reduced fertility both in litter size and in sperm viability

>Increased congenital defects such as cryptorchidism, heart defects, cleft palates.

>Fluctuating assymetry (such as crooked faces, or uneven eye placement and size).

>Lower birthweight

>Higher neonatal mortality

>Slower growth rate

>Smaller adult size

>Loss of immune system function.

Well said!!!
Also, what has been missing from the discussion is the non-mendelian patterns of inheritance that do not cause on-off damage and do not skip generations.

There are many other considerations of the harms of inbreeding (even when fresh "outbreeding" is introduced) that weaken the population as a whole.

I'll add more later. But thanks for throwing the flag!

Matt

I've yet to weigh in here, but I might as well..This post is IMO and should be taken as so..
RB has some good points, but overall I must agree with CH13. Recessive genes, like hemophiliai humans, do not manifest until mated with another recessive hemophilia gene. It doesn't mean the gene doesn't exist and is not deleterious to the carrier. In humans, luckily, usually the out come is only 1 hemophiliac. In animals where most produce more than 1 offspring, it means all offspring will manifest the recessive trait..Now that could be a good thing if you're looking for the elusive "piebald Indy", but I must posit that it is not, overall, a good thing(except maybe for your pocketbook if you're the lucky breeder!)
Jeff points out below further deliterious effects of inbreeding.
I certtainly will bow to the years of success of both RS and RB in their breeding efforts and success but I cannot endorse inbreeding as a routine practice..Diversity always strengthens genetic lines and should be encouraged by keeping good records of breedings and breeding lines which has been sorely lacking over the years of Drymarchon breeding..
Regards, CG
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Carl W Gossett
Garage Door Herps
Monument,Colorado...northern territory of the Great Republic of Texas

Dear Mad Matt,

I don't think anyone understands your post, certainly I don't. With complete respect, I am not a fan of statements and posts which use complicated scientific terms to justify a conclusion, but which don't define the terms or explain how the conclusion is reached.

I can think of two examples of non-Mendelian genetics, sex-linked genes and mitochondrial genes.

Many people don't know that our mitochondria (the organelles in our cells which generate chemical energy as ATP) are passed to us from our mothers but not from our fathers. Mitochondria contain their own DNA, and don't sexually reproduce. We all have our mother's mitochondria.

Sex linked genes are genes on our X-chromosomes. In male humans which only have one X chromosome, there are only one copy of the associated genes, whereas in females there are two copies. Snakes have a somewhat different sex-chromosome makeup (not X and Y like in humans).

Neither of these instances typify "Mendelian" genetics. Nonetheless, I fail to see how this scientific "term dropping" has any significance for the arguments I have been making. Since you have offered to elaborate on your statements, I would greatly appreciate it. Perhaps I am missing something, and maybe with further elucidation we all can learn something.

Robert Bruce.

You don't understand that there is a large cache of genetic damage that we all have, even the healthiest of individuals, in both snakes and humans.

Inbreeding or linebreeding is a sure way to amplify this damage.
Inbreeding changes this to an invisible problem within the individual to a very visible one with the population.

I am a little short of time this weekend. I do not have time to elaborate.

Again, the manner and cause of mutations is a moot point.
It doesn't matter if inbreeding does not cause mutations.

It does matter that inbreeding causes such rediculous amplification of genetic damage from an individual level to a population level.

Sorry, most of us here care about the species, we have a limited population of captive individuals. Our common good as a group of current and future indigo keepers depends on responsible husbandry and breeding practices. This conflict of interest may not be good for marketing efforts of inbred snakes.

My apologies if that is the case.

Dear Mad Matt,

I do indeed understand that we all harbor defective genes, snakes and humans.

In my post below (Fallacy #2) I show how limited inbreeding does not amplify the abundance of defective genes in populations (as you state) but actually decreases the gene frequency of defective genes.

Your insinuation that my motives for my arguments here are simply to forward my own marketing efforts of inbred Easterns is absurd. I have already clearly elucidated my motives. It is my contention that we can help the wild population of Eastern Indigos by the way we do our captive breeding, and this includes the use of limited inbreeding. Your "marketing" argument is an ad hominum attack, considered innately fallacious by modern philosophers.

Robert Bruce.

Hi "Robert",

Your response Fallacy #2 doesn't show that inbreeding does not amplify genetic damage. In your mind I know that the particular defect that you can see is not being passed on, but you are ignoring the point that you stated you understood about the remainder of genetic damage that we carry.

I guess you are assuming there is only one defective gene and you have the power to see it because it is expressed. Thats not the case.

Even the healthiest individuals carry multiple defective genes sometimes that are unique to either ourselves or our family. They are never seen because without inbreeding, the chance for these rare genes to be paired or homozygous is extremely remote.

For humans the number is placed conservatively at 4 recessive lethals per individual(an outwardly helathy individual not showing signs of weakness)

When you inbreed to avoid one defect, a person unwittingly selects other defects to be magnified. I am not making this up this is basic population genetics. It is the reason we have sexual reproduction rather than asexual reproduction.

Our ability to witness the genetics of an individual or a species is very limited. You posts indicate that you "know" that an animal is inherently free from defects by looking at it, and that its genetics should magnified through the population. Thats not the case.

Regardless of good intent, not following good breeding practices affects us all. We don't want dwarfed, stub-tailed, bug-eyed regurging indigos(leucistic rat snakes anyone) that are high red.

On the marketing issue, I could be wrong, but I invite you to consider that people are paying very close attention to you and your logic is extremely difficult to follow. If I was wrong I am sorry but I patiently await a contingent response.

Matt

Dear James,

The weakening of animal lines you are speaking of is a result of repetitive inbreeding, or "line breeding" as you earlier mentioned. I am not a proponent of line breeding in Eastern Indigo Snakes because there is no good reason to do it. Line breeding is used to obtain pure strains for scientific study. There is no need for pure strains of snakes amongst captive breeders. Repetitive inbreeding can lead to rapid gene loss in animal populations, weakening the genetic diversity of these populations.

When inbreeding is followed by outcrossing, animal populations retain their vigor. This is the form of inbreeding that can be useful.

You also mentioned "cell passaging" meaning cell cultures (grown in petri plates). These cultures typically lose function and viability with repeated generations. This is because, firstly, that there is no selection occuring for cells which retain traits of the animals from which they are derived. Cell cultures don't grow hair, don't sexually reproduce, don't hunt for food, don't think, and on and on. When there is no continued selection pressure for necessary traits, these traits are lost over time.

The other reason that cell cultures sometimes lose function is that they are frequently derived from mutant, cancerous or virally transformed cells.

I should also point out that in nature, inbreeding-outcrossing is the general rule. If we strictly avoid inbreeding, then our captive animals will be reproducing in a manner which does not emulate wild populations. Limited inbreeding is also beneficial to wild populations, which I will comment on later.

Robert Bruce.

Dear Robert,

Thirty years of leagal protection = 30 years of genetic "funneling". How truly diverse are the animals we're breeding? I inquired about a breeder's indigos in Washington, to find some unrelated animals, and it turns out his came from a breeder 10 miles from me. I inquired about a female from someone in Cali, turns out it was related to the "father" of the snakes I bought from you.

In some respects the species has already been being linebred for the last thirty years.

Dear James,

I am pretty much with you here.

I have tangled with the idea of an Eastern Indigo registry and an associated lineage database, for quite a while. I have the means to do this. What has held me back is the sensation I have that we won't be able to track backwards more than one or two generations. We will be reliant on detective work to try to uncover breeders and the sources of their animals. Some of these breeders are dead. Many or most others wouldn't have records and would have forgotten the details. In many cases, we might not even be able to track down some breeders. If any animals had suspicious origins, is the breeder going to be cooperative?

How few or many original Eastern Indigos make up the ancestry of our current captive population? If we knew the answers, what would we do?

While I don't think the genetic diversity of our captive population is as limited as others speculate, knowledge is never a bad thing. It would be nice to know (or at least know better than we do now).

Robert Bruce.

i suppose we can continue to go round and round on this month after month, but the truth is most of us have absolutely no idea what the genetics of the "captive population" looks like. that is, we don't have a clue what degree of genetic diversity we are dealing with in this country.

some feel/believe/think/opine that most of the current stock come from very few idividual snakes. if this is the case then everyone is inbreeding their indigos.

others have chimed in that there is the possibility of an allelic migration into the captive population, especially on the east coast. if this is the case then some of us are unwittingly inbreeding while others are not. but once again -- who's keeping track? how far back are any of us able to track our indigos? if known, how many are willing to divulge where their animals came from. with a few exceptions, i've run into many people holding their pedigree cards pretty close to their chests.

once we have the procedure down for looking at individual genotypes, it will be interesting to see who will step up and have their breeders genotyped. there will be fear of exposing rare (and therefore newly "acquired" animals) and genetically diverse breeders. good because they are diverve, bad because they may have been acquired illegally. there is also the fear of exposing closely related breeders. there go the profits.

hopefully, with voluntary genotyping, there will also be fair-trade agreements and an attempt to outcross as much as possible.

just a couple thoughts on the subject,

matt

Excellent and polically correct for the forum censors, Matt
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Carl W Gossett
Garage Door Herps
Monument,Colorado...northern territory of the Great Republic of Texas

Jeff, in his reply to my original post on the virtues of inbreeding (OKay Robert, I'll bite...), exposed a second commonly held fallacy. This fallacy is the belief that inbreeding leads to increased mortality rates and is therefore harmful to the population (wild or captive).

Yes, inbreeding can result in a greater mortality rate in progeny from related parents. This is because there is a greater chance that such progeny posess two defective copies of specific genes required for survival. Without at least one normal gene, some of the offspring inherit a lethal condition, and die.

Captive breeders can expect a somewhat greater mortality rate when related animals are bred together. The more closely related the parents, the greater the chance of mortalities in the offspring. This may be evidenced as infertile eggs, eggs that go to full term but don't pip, hatchlings that die shortly after hatching, and so on. The more heavily laden the parents are with defective genes, also the greater chance of mortalities after inbreeding.

The fallacy here is the direct assumption and conclusion that if there are more mortalities, it must be bad.

When a mortality occurs due to a defective gene, that incidence of the defective gene (in the dead individual) is removed from the population. In the remaining live animals, the gene-frequency for the defective gene (the percentage of that particular gene that is defective in the population as a whole) goes down. This is good. We want minimal incidences of defective genes in our captive population, right?

If we want the incidence of defective genes in our captive populations to be minimized, then it is important that we perform limited inbreeding. As we see mortalities, the remaining population is necessarily strengthened because the gene frequency of defective genes in the population is reduced.

Again, I am not advocating repetitive inbreeding (line breeding) and there is certain virtue in attempting to maintain genetic diversity in captive and wild populations. Nonetheless, limited inbreeding (inbreeding followed by outcrossing) has clear virtues. I have now elucidated at least three of these virtues.

Robert Bruce.

Mortality in vitro just stops that specific animal from producing. It does not stop the breeder from trying to cross the same 2 F1's again to achieve a desired result, be it coloration, feeding habits etc. The fact remains inbreeding, of any amount, perpetuates faulty genes, whether physically expressed or not, in any 1 given any animal, the genetic defect may live on to be expressed in the next generation.
The best point of these discussions is addressed above, that being some method of voluntarily limiting, registering, and recording each breedings lineage to maintain divesity and avoid repetive breedings to the same genetic pool..East Coast, West Coast, Mid-West, we have very little info on who's stock the animals originated from..
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Carl W Gossett
Garage Door Herps
Monument,Colorado...northern territory of the Great Republic of Texas

Dear Carl,

I think you might be misusing the term "in vitro." In vitro means not in a living entity, so there is no meaning to "mortality" in context with in vitro. In vitro may refer to chemicals, extracts of cells or viruses, test tubes etc., but not to living forms of life. Conversely, in vivo refers to things within living entities.

With all respect, you are restating a fallacious belief, not a fact, that all inbreeding leads to the accumulation of defective genes in populations. No amount of restating fallacies will make them facts.

When individuals with defective genes are removed from populations (by mortality as I was arguing in "Fallacy #2" then incidences of those defective genes are removed from the population, and the gene frequency of those defective genes goes down in the population (not up as you state). The mortality serves to remove defective genes, not perpetuate them.

There is nothing to stop breeders from repetitively breeding related offspring to one another. To maintain the health of captive populations, while still benefiting from the virtues of limited inbreeding, breeders should follow up instances of inbreeding with instances of outcrossing.

While it would be nice to know where our animals came from, and to what extent the gene pool of captive Easterns is limited, I don't see much positive benefit in this knowledge, except maybe to argue that input to the captive population from the wild population would be good. Without this information, all we have to do for the health of the captive population is rotate breedings. Male #1 with Female #1 and Male #2 with Female #2 one year. Male #1 with Female # 2 and Male #2 with Female #1 the next year. If we can loan animals to one another to encourage diversity, this is even better. If one set of pairings is inbreeding and the other is outcrossing, then we have what is needed for a healthy population.

As breeders, we should always know when we are doing inbreeding and when we aren't. Although Matt Rand argues that we may already have an inbred captive population (and not know it) I doubt that what we have is too inbred. Others have already indicated that wild Easterns were still freely coming into the captive population in the 80's and even 90's. Confiscated animals are still entering the captive population today.

If anyone sells an inbred animal to another person, that information should be communicated. I personally would never sell an offspring resulting from inbreeding to another person without specifically informing that person of the details of the cross. My captive collection of Easterns is the largest and most genetically diverse in the country. No one that has received animals from me owns knowingly inbred individuals, unless they were specifically told of this by me before the sale.

Robert Bruce.

You're almost correct.."In Vitro" means living tissue as in "egg" outside another living organism, not a chemical or other non living organism, and technically is a term we use in research, as in "research in vitro" meaning research in the egg.. I should have said "in the egg" to make my meaning clearer, sorry if that caused confusion.."In Vivo" means an actual living creature(actually testing on the living creature)..So the posit that inbreeding leads to more infertile eggs, in egg deaths, failure to pip, etc was what I was referring to..And just because the egg dies does not mean the defective gene is gone, that would be a mutation of a gene that would be eliminated, not a parental gene..

Now to the other assertion of a very limited captive gene pool. I thought I was big time when I had 11-12 Easterns 6 years ago. You and Rob Seib have 20-30 breeding Easterns (if rumor is correct)Not sure about Steve, but maybe he's in that range too..

Since the rest of us are lucky to have 1 breeding pair, the assumption that a very significant portion of the captive gene pool originates with you guys is not hard to believe..I have very serious doubts of any "blue gophers" coming out of the wild anytime after the '70's. I can't prove that, nor can anyone disprove it..But back in the 70's (I'm that old!) you could buy, before 1973, Easterns for a couple of bucks per foot! I doubt too many people would poach for prices like that, given the penalties involved with the ESA if caught..

Therefore the need for an accurate lineage recording and report, so as not to continually breed back to the same line is even more important..It seems that you believe this by your last post..So can you provide written pedigrees of you product? It seems we need an AKC type registration system for Dry's given the fact that 99.9999999% would rather freeze a cross-bred animal if we are to believe the tone this forum usually takes when that issue appears..That would be totally voluntary of course..And would Doug T be willing to be the keeper of records? Or anyone else? We would have to start with now..Couldn't prove last year or the year before..I would see RS #1F x #6M F1 as a start for naming lineages, you the same, RB #2F x RS #3M F1 if you guys worked out a breeding loan as you both live in CA..As for me, there's not another Dry breeder in 600-700 miles! And I haven't produced since '02 when I had to eliminate all but 1 pair and haven't had the time/luck to stay serious in the mix..

Come back?
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Carl W Gossett
Garage Door Herps
Monument,Colorado...northern territory of the Great Republic of Texas

Dear Carl,

I (personally) have never heard of the term "in vitro" used to describe anything within a live egg, except for one exception that I mention below.

In science, the term "in vivo" is meant to describe operations with or within living matter.

In a simplistic but true way, the term "in vitro" to a biochemist means "everything else that does not qualify as vivo." This in reality means any processes that are carried out in the absence of living cells.

Here is the line where an experiment goes from in vivo to in vitro. If an experiment is performed in a test tube with live cells, it is an in vivo experiment. If the same experiment is performed in a test tube with crushed or broken cells, or a cell extract, the experiment is in vitro.

Scientists across the world use these terms in this way. Thus anything referring to a live egg, or to the process of going from life to death (mortality) could not be considered in vitro.

The only exception to this usage that I have heard of came when Medical Doctors (naturally) used the term (incorrectly) to name the process of live fertilization of human eggs outside the female reproductive tract. In Latin, in vitro means in glass (in a test tube) and this is how in vitro fertilization got its name. But to a biochemist (and pretty much everone else) the fertilization process involves living cells and thereform must technically be an in vivo process.

If you go to en.wikipedia.org/wiki/In_vitro you should see the definition of in vitro as I am using it.

Doctors would more correctly have named the in vitro fertilization procedure Ex Utero Fertilization, or something of that nature.

Robert Bruce.

In Vito means outside of a living organism as in the egg or a group of cells in a petri dish..It does not have anything to do with non-living matter. It specifically is living matter, not chemicals. I clarified the statment in the above post and it stands. In Vivo means testing in a living creature, not test tube of cells, but a whole, living creature..
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Carl W Gossett
Garage Door Herps
Monument,Colorado...northern territory of the Great Republic of Texas

I couldn�t help putting my two cents here. In vitro refers to a situation where the data are collected out of a natural environment (i.e., artificially manipulated in that respect). This can refer to noncellular systems such as enzyme kinetics in a test tube, but it can also refer to living cells taken out of the systems where they are naturally found (e.g., transformed cell lines, or in vitro fertilization of otherwise perfectly normal ova and sperm). With respect to inbreeding, there are a some misunderstandings here. There are certainly a lot of problems present at high frequencies in indigos: spinal kinks, infertility, malformed gastrosteges, missing or malformed ribs, dwarfism, shortened tails, etc. The idea that some inbreeding will rid the population of the alleles responsible is not accurate, as this takes extreme inbreeding, with high levels of drift layered on top of it. The effects are rarely good, even if the population survives. You need look no further than the cheetah to illustrate that point. The post yesterday hypothesizing that these alleles are maintained in the population because in the heterozygous condition they are somehow beneficial seems rather farfetched. The maintenance of the sickle cell allele because heterozygotes are resistant to malaria is such a rare case of heterosis that it is one of the only examples ever cited. It seems no more plausible that any of the loci responsible for these conditions are advantageous as heterozygotes than it is to invoke that explanation for human dwarfism, albinism, etc. The high frequency of these conditions in indigos is almost certainly a case of founder effect. And like the well known examples of this in humans (dwarfism in Amish, tay-sachs in eastern European jews, blindness on Tristan da Cunha, etc.), unless the population goes through extreme and repetitive bottlenecks, these deleterious alleles are not going to disappear. The problem is that if there are multiple severe bottlenecks, it is as likely as not that the entire population goes extinct. It is absolutely ludicrous to think that reducing the natural genetic heterozygosity any more than it already has been. Even if one ignores all the possible genetic problems that could arise, problems that are seen in every heavily inbred organism, such as purebred dogs, there are other problems. It is entirely possible that many large populations of Tasmanian devils will become extinct in the not too distant future because of the out of the blue appearance of a new virus that causes facial tumors and is running amok in the devils precisely because of their lack of genetic diversity because of founder effects. Genetic drift is constantly eliminating alleles from populations, and the loss from small populations is much faster than new ones are being created by mutation. Trying to counter this problem in small isolated populations where immigration is not bringing new alleles in is one of the dominant themes in conservation biology today. I am speechless that anyone would argue that even limited inbreeding of indigos could be a good thing, in any possible way.

I think that's "enuff said"...
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Carl W Gossett
Garage Door Herps
Monument,Colorado...northern territory of the Great Republic of Texas

Dear Steve,

Thank you for joining this discussion. I will not be able to address all of the points/arguments you have made in a single reply, so I apologize.

It seems to me that there are three viewpoints here, two are the extremes and one is the middle ground. Even though it may not seem so, I am taking the middle ground viewpoint.

On one extreme, as you seem to argue, no amount of inbreeding is good in any circumstance.

On the other extreme, as you and others seem to think I am coming from, all inbreeding is great and the more the better.

My viewpoint is that the use of limited inbreeding by snake keepers has virtues for captive populations of Eastern Indigo Snakes.

Certainly, intensive inbreeding can have profound and many times negative effects on populations. But, it is wrong to argue that because repetitive inbreeding can be harmful, therefore limited inbreeding is certainly harmful. Your arguments against inbreeding are all justified by examples of repetitive and intensive instances of inbreeding.

The last statement of your post above claims, in a somewhat emotionally charged way, that any inbreeding is tantamount to the plague, and you are "speechless" that anyone would voluntarily cause inbreeding in even the most limited manner.

Obviously, inbreeding occurs in wild populations all the time. If even one instance of inbreeding is so harmful, then I would suggest that the primary tactic of wildlife biologists to "save" threatened populations would be to (1) catch all wild animals and tag them with satellite radio telemetry transmitters and (2) send out teams of wildlife biologists to separate any animals that were related to each other if they got close to each other during breeding season.

I reallize that this is a rhetorical argument. Clearly, wild populations at the minimum tolerate limited inbreeding. We don't send out teams of biologists to prevent any instances of inbreeding in the wild. Limited inbreeding can't be as bad as you indicate.

If wild populations can at least tolerate limited instances of inbreeding, then why can't captive populations? If it occurs in the wild, then why should we go to great lengths to prevent any occurance of inbreeding in captivity? We would be making our captive populations live up to standards that are not lived up to in wild populations.

There are clear arguments that I will make later that at least some inbreeding can not only have beneficial effects on populations, but even intensive forms of repetitive inbreeding can save(and have historically saved) populations from extinction. You may know where I am going here.

Finally (for this post) you have mis-read my recent argument about fallacies of inbreeding. I didn't say that we should engage in inbreeding practices in order to "rid" our populations of defective genes. What I stated is that there is a commonly believed fallacy that because inbreeding can lead to increased mortality, that it is therefore bad. I have tried to show (although not everyone is buying it so far) that with mortality, incidences of lethal defective genes are removed from the population, and the gene frequency of those genes as a result, goes down in the population.

I am simply saying that it is wrong to argue that inbreeding is bad because of increased mortalities. The mortalities are helping the population as a whole. Ridding populations of defective genes is not what I am striving for here. I am pointing out that using the mortality argument to justify strict avoidance of limited inbreeding is a fallacy.

Robert Bruce.

Hi Robert, I dont really have time for a long post, as I have a lab to teach in 15 minutes. But the argument that because there is inbreeding in natural populations that it is either a good thing, or that that means it must not be so bad, is not true. Everything from fungi to apes have evolved myriad physical, physiological, and behavioral mechanisms to avoid inbreeding. This, even at the consequent cost of a reduced reproductive rate! Such things would never evolve if inbreeding were not detrimental. The bottom line is that organisms maximize their fitness by trying to leave the most offspring that are capable of surviving to reproductive age and reproducing. Fitness is not simply how many ova can you fertilize. avoiding inbreeding apparently is more important than attaining more matings if the goal is to maximize fitness, or such inbreeding avoidance mechanisms would never appear. Fathers would mate with female offspring before they left the nest or den, and siblings would be breeding as soon as they were capable. This doesnt happen except where we force the issue by keeping mice, for example, in cages with descendent young where no dispersal can occur. Or by doing the same in indigo snakes. Yes, there are occasionally deleterious alleles that can be lost by inbreeding, but it is the exception rather than the rule. And yes, there is an optimal level of outbreeding, severe outbreeding is somewhat less desireable than some moderate amount, termed optimal outbreeding. But our indigo population is small enough that if we outbred every cross as much as possible, we could probably not even approach this level of optimal outbreeding. I would not be terribly surprised if this were true even in wild populations. And "overly" outbred animals are still a much fitter proposition than overly inbred ones. And this is true whether you are talking about the appearance of developmental problems and defects, like poor fertility in cheetahs, or resistance to new pathogens, such as in the tasmanian devils. Now i really have to run.....

Dear Steve,

I think that you are mixing up the value of outcrossing and interbreeding in nature with the avoidance of inbreeding.

Sexual reproduction is nature's number one mechanism for getting together traits from separate individuals into single individuals. Clearly there is benefit to living organisms when they can exchange genes and produce progeny with new and unique combinations of genes and traits. But you are taking this too far to conclude that nature has evolved to strictly avoid inbreeding.

Many plants have flowers that, to a high degree, pollinate themselves. The avenue is open for cross pollination, but the majority of offspring are inbred.

Bacteria reproduce asexually the vast majority of the time, with sexual reproduction a possibility, but a much less frequent occurance. Again, the avenue exists for outcrossing, as an evolutionary advantage, but outcrossing isn't strictly enforced.

Nothing has evolved to prevent most animal species from inbreeding. Siblings or family members could share pheromones which repel each other, for example, to prevent inbreeding. This is generally not the case.

The emphasis in nature as I see it is to promote the possible exchange of genetic material in unrelated organisms, but not to enforce that only unrelated organisms can mate (avoid inbreeding). There are a few (a small number) of instances, particularly in bacteria, where only different mating types can sexually reproduce, but this is the exception in nature, and not the norm. Apes or cheetahs or tasmanian devils posess no mechanism to prevent inbreeding. They simply posess mechanisms to enable outcrossing and exchange of genetic material between unrelated organisms, so that individuals with unique genetic combinations can result.

Robert Bruce.

Hi Robert,

"Nothing has evolved to prevent most animal species from inbreeding. Siblings or family members could share pheromones which repel each other, for example, to prevent inbreeding. This is generally not the case. "

hi Robert, I dont really have time to address this much with the end of the summer semester coming, I originally intended to put in a single post. Im not a geneticist, but I am an evolutionary biologist and have spent a great deal of time studying the evolution of mating systems, including the issue of inbreeding, so I can tell you that youre dead wrong about the inbreeding avoidance mechanisms. Of course limited inbreeding takes place but it is always limited by mechanisms to avoid it. Most monoecious organisms do NOT fertilize their own gametes, even though this would be the most expedient way to produce offspring quickly. Why? Because even though they would produce more offspring, those progeny would have less chance of resisting disease outbreaks and would have more problems due to deleterious recessive alleles. And many plants have complex ways of blocking related pollen from fertilizing their ovules, so it is most definitely not the simple picture youre imagining. Vertebrate avoidance of inbreeding is mostly of the behavioral type but the mechanisms are very strongly developed. It is very rare indeed, that brother and sister cheetahs would ever mate. With all due respect, you dont seem to know the literature too well, and seem to have an agenda you want to promote. Or maybe you are trying to justify or rationalize the level of inbreeding in your snakes, and all of our indigo snakes. I cant spend any more time debating this, I just wanted to pitch in on something I do know something about. Anyway, theres not much we can do to avoid inbreeding in our snakes at probably very high levels, even when we think we are outcrossing them. None of us really have much information about our snakes more than a generation back. Just because I have bred a male that came from Robert Seib to a female from Doug Taylor, I cant be sure that the grand parents or great grand parents of the two snakes arent the exact same snakes. So in a sense it is a moot point for indigo snakes, unless you are performing crosses of very closely related snakes (like people do to try to bring out rare recessive traits, like the albino blackheaded pythons now), which would be a terrible idea in my opinion.

Dear Steve,

This thread is about two fallacies that I have commonly heard about inbreeding. As far as I can tell so far, you are addressing everything but these two fallacies. I haven't heard a single argument from you which weakens my position regarding exposing these fallacies.

You also seem to spend effort making up motives for me when I have already clearly stated my motivation for this discussion.

Because you claim that you "know" the literature (and you claim that I don't) and because we are talking about Eastern Indigos, I have a question for you. Since you state that avoidance of inbreeding is so universal in nature, if a male Eastern Indigo were to cross paths with a female Eastern Indigo during mating season, and they happened to be siblings, what mechanism(s) would prevent the two from mating?

Robert Bruce.

Ok, Robert, Ill bite one last time, then I really have too much work to do. Yes, I do know the literature, I do this as a profession, not a hobby, and would be unemployed if I did not! I have no idea if you do or not, but you continuously are espousing ideas that are supported by no empirical data and you do seem oblivious to hundreds of peer reviewed published papers specifically on inbreeding depression and avoidance in a wide variety of taxa. I am totally in the dark as to your motives to do so, but it does bewilder me. I will simply refer you to a handful of the many hundreds of papers, and you can then follow their citations to others which will explain inbreeding depression and inbreeding avoidance. Ill give you one quote from the abstract of a paper on inbreeding in flycatchers: Inbreeding was rare, to the extent that we detected only 1.04% of 2139 matings over 18 years that resulted in offspring with a non-zero inbreeding coefficient, f > 0. When it did occur, inbreeding caused a significant reduction in the egg-hatching rate, in fledgling skeletal size and in post-fledging juvenile survival, with the number of offspring being recruited to the breeding population from a nest of f = 0.25 being reduced by 94% relative to a non-inbred nest.” This single statement simultaneously refutes both the contention that animals don’t avoid inbreeding, and that it does not have detrimental consequences. It is from Kruuk, Sheldon, and Merila. 2002. Severe inbreeding depression in collared flycatchers (Ficedula albicollis). Proc. Biol. Sci. 269: 1581.

I have pulled a few other papers from either the primary literature or reviews to get you started reading about both inbreeding avoidance and inbreeding depression. With specific reference to indigo snakes, noone has attempted to study them in this way. Few have studied any reptiles in this respect but I have included some references that discuss what we do know already. I didn’t bother including any about plants, but if you want them I will pull those papers at a later date for you, I assure you there are plenty of them:

Clutton-Brock. 1989. Female transfer and inbreeding avoidance in social mammals. Nature 337: 70.

Clarke and Faulkes. 1999. Kin discrimination and female mate choice in the naked mole-rat Heterocephalus glaber. BioSci. 266:1995.

Pusey. 1987. Sex-biased dispersal and inbreeding avoidance in birds and mammals. TREE 2:295.

Burke. 1993. Adaptive value of sex determination mode and hatchling sex ration bias in reptiles. Copeia 1993: 854.

Madsen, Stille, and Shine. 1996. Inbreeding depression in an isolated population of adders Vipera berus. Biol. Cons. 75:113.

Crnokrak and Roff. 1999. Inbreeding depression in the wild. Heredity 83: 260.

Ralls, Ballou, and Templeton. 1988. Estimates of lethal equivalents and the cost of inbreeding in mammals. Cons. Biol. 2: 185.

Buechner. 1987. A geometric model of vertebrate dispersal: tests and implications. Ecology 68: 310.

Potts, Manning, and Wakeland. 1994. The role of infectious disease, inbreeding and mating preferences in maintaining MHC genetic diversity: an experimental test. Phil. Trans. R. Soc. Lond. B 346:369.

Berger, Negus, and Day. 1997. Recognition of Kin and avoidance of inbreeding in the montane vole, Microtus montanus. J. Mammalogy 78: 1182

And not to let you think that inbreeding avoidance does not take place in apes, cheetahs, or Tasmanian devils (which you unequivocally stated), I am also sending you to these three examples that address all three taxa. Note that Tasmanian devils have not been studied in this respect, here is another carnivorous marsupial example of what will certainly be the case in devils too:

Starin. 2001. Patterns of inbreeding avoidance in Temminck’s red colobus. Behaviour 138: 453.

Cockburn, Scott, and Scotts. 1985. Inbreeding avoidance and male-biased natal dispersal in Antechinus spp. (Marsupialia: Dasyuridae). Animal Behaviour 33: 908.

Durant, Kelly, and Caro. 2004. Factors affecting life and death in Serengeti cheetahs: environment, age, and sociality. Behav. Ecol. 15: 11.

"Robert"

With rare conditions that creep up, eliminating the unhealthy indviduals from a population helps from increasing the allelic frequency but it does not do much to REDUCE the allelic frequency. It takes many, many more generations to effectively reduce the heterozygotes when the allelic frequency is lets say 1% or below. This would fit having a rare trait that we want to get rid of.

But to jump to inbreeding as the only option or as something better than breeding obviously sick animals is quite a jump. I hope you can understand we are having a great deal of trouble following your logic.

Jack and Jill are going to get married. Jack has cystic fibrosis. So Jill marries her brother. This is OK because Jill's brother looks healthy. We know that Jack and Jil host a lot of rare mutations that are will stay invisible(unexpressed) if they were to never breed.
The simnple instance of them breeding allows every deletrious allele they carry( about 4 recessive lethals) to be paired and expressed in progeny. Even with the non-affected heterozygotes, the allelic frequency went up dramatically. Now the population has new pressures imposed on it.

But, There are other guys for Jill. You see?

For the sake of the population we all agree that Jack shouldn't breed with Jill. But the hypothetical would only be reasonable to consider if we had three individuals. There are more than three lines out there.

Perhaps, I am just missing something.

Matt

then why not indigo snakes?

http://en.wikipedia.org/wiki/Blue_People_of_Kentucky

Dear Matt,

I do realize that many people will be having difficulty following my logic. The problem is confounded because I am attempting to make arguments that contradict messages that many of us learned in grade school, and believe inherently. When I started this topic in the earlier thread "Virtues of Inbreeding" I thought long and hard because the logic and arguments are so complex.

The problem is also confounded because I am trying to take logical steps piece by piece, and most people are trying to jump forward to where I will be going with this.

For this thread "Fallacies about Inbreeding" I am not trying to convince anyone (so far) that we should use inbreeding to accomplish anything (but I will later). I have seen two primary fallacious arguments put forward by others that I am meaning to dispel.

The first fallacy is that inbreeding causes the generation of defective and deleterious genes (alleles or "forms" of genes). Inbreeding does not create new defective alleles. I don't know if we are all there or not yet, but inbreeding can cause these genes to become apparent within populations, and that in the absence of inbreeding, the conditions caused by the defective genes may never be seen.

The second fallacy is that the mortalities seen after inbreeding mean that inbreeding is bad. I have tried to show that the mortalities cause a reduction in the gene frequency for defective lethal genes, not an accumulation of these genes as many seem to think.

In my original post "Virtues of Inbreeding" I stated that the only valid concern and argument against inbreeding is related to gene loss that accompanies extensive inbreeding in populations. I am trying to dispel these other fallacies so as to focus the attention back on gene loss.

I also intend to show (and have already shown) that inbreeding can be used to uncover and propagate unusual traits in populations, and that this can be beneficial for captive and wild populations (for different reasons).

So, if there are positive attributes to inbreeding, and the only concern is gene loss, can we have the best of both worlds? Can we perform inbreeding in captive populations in such a way so as to obtain the positive aspects (uncovering and propagating rare and unusual traits, helping to select out unwanted traits) and to avoid the negative aspects (unwanted gene loss). I believe that the answer is yes, and by hypothetical examples that I have yet to put forward, I will try to demonstrate how.

It is important that participants in these threads try not to go too far forward in making more out of what I am saying, than what I am actually saying. We will have a chance to do that later. For this thread, there are two fallacies that I have pointed out. If you think that I am wrong about them specifically, try to shoot them down. When the dust settles, we can take more steps forward in logic and discussion.

I do thank you all for your input, as I can see you are all well meaning and truly concerned about the Eastern Indigo, and other threatened and endangered creatures.

Robert Bruce.

Must be awful lonely in that hole your digging. How's that web site with all your snakes coming? I'm sure you'll need some powerful new technology to handle the demand for your Indigos now. Can we get $100 off for the inbred ones? Not that your in it for the $ or anything.

Hi Robert,

This is not just a hypothetical argument. You have an immense degree of power to create problems for indigo keepers later down the road from well-intentioned yet poor husbandry practices.

There is no dust, as you say. Your most basic assumptions are extremely strained and amorphous. None of your posts dove-tail in the slightest. Your confusion as you write is apparent, but please understand, it is also frightening to us who want good stock ten years from now.

This is before you extrapolate from these embryonic thoughts into how you are going to design a better snake from these assumptions.

Believe what you will, but most of us do not want to see a market created for wild-caught snakes (Legal or illegal).
We need a captive-born population of animals that has not been someone's first experiment into genetics. This population may not be perfect, but it is all we have.

If we want the captive-bred popualtion to be credible or representative we need good husbandry practices. Some inbreeding has undoubtedly occurred. We are already seeing strange indigo specific traits developing. Further inbreeding just magnifies this.

We do not want the captive born population further compromised by misguided though well-intentioned husbandry.

Having people post about how they just received an apparently healthy high red pair of babies for you will not help this argument. WE know that the apparently healthy babies produced by inbreeding will start to cause headaches when those babies and their babies breed. What will be the new nasty traits that will be expressed by these otherwise healthy looking "high-red" indigos?

Or, Perhaps the market for high red disappears because the reputation of the high red animals is synonymous with bad stock?
None of us want to be seen responsible for that. Right?

Matt

Dear Matt,

You are inventing problems with my breeding practices. As I have already stated, it is important to me that we maintain as much genetic diversity in our captive Eastern Indigo population as we can. I do expect the captive population to diverge genetically from the wild population, and certain instances of gene loss are OK with me, but on the whole I want to minimize gene loss.

I want the best of both worlds, as I have stated. I want to uncover and propagate rare and unusual traits in Eastern Indigos while at the same time preserve genetic diversity. I think that this can be done, and I intend to show how. When you and others skip ahead and invent motives and arguments for me, before I have gotten there myself on this forum, then confusion really arises. If you want to keep the confusion to a minimum, try to focus on the subject that I put forward in the thread. In this thread, the subjects are what I see as two commonly held fallacious beliefs. When these beliefs are invoked, going anywhere on the subject of inbreeding becomes impossible, so my first task is to dispel them. I have already stated these fallacious beliefs at least twice, so I see no need to repeat it here.

Before you speculate on all of the damage you think I am or may be doing, just look at the animals I have as breeders. I have animals from Chuck Elliott, Robert Seib, Steve Fuller, Hans Koenig, Don Hamper, Howie Sherman, Jimmy Mabe, and Greg Maxwell, and I continue to seek new bloodlines to add. I don't want rampant gene loss in captive animals, quite the contrary. I brought the whole subject up didn't I?

I am trying to focus the attention of keepers of Eastern Indigos on gene loss as the only serious problem with inbreeding. By exposing two commonly held fallacies, I hope to redirect the attention regarding inbreeding onto the subject of gene loss, and away from the two misleading fallacious arguments I have cited.

You have, to your credit, tried to invent a model (Jack and Jill) to show the problems with inbreeding, but as you mentioned yourself, the model is not representative of a typical population (wild or captive). You have claimed that my arguments are hard to follow (understandable) and that my "confusion is apparent" (crossing the line into insult and unfriendliness).

I will next present a model that more accurately depicts population dynamics, and will try to show more clearly how mortalities associated with inbreeding lead to the DECREASE in the gene frequency of defective and deleterious genes (alleles).

Robert Bruce.

Hi "Robert"

I have been a little busy this week. No time to write.

I am scared, and now I am amused too when I read your posts.

Until later.

Matt